An evo-devo geek's scientific meanderings

Month: November 2011

Make science into a game, and you’ll not only entertain thousands of people, but may also solve some of the toughest problems in your field.

Algorithm discovery by protein folding game playersFiras Khatiba, Seth Cooperb, Michael D. Tykaa, Kefan Xub, Ilya Makedonb,Zoran Popovićb, David Bakera,c,1, and Foldit PlayersFoldit is a multiplayer online game in which players collaborate and compete to create accurate protein structure models. For specific hard problems, Foldit player solutions can in some cases outperform state-of-the-art computational methods. However, very little is known about how collaborative gameplay produces these results and whether Foldit player strategies can be formalized and structured so that they can be used by computers. To determine whether high performing player strategies could be collectively codified, we augmented the Foldit gameplay mechanics with tools for players to encode their folding strategies as “recipes” and to share their recipes with other players, who are able to further modify and redistribute them. Here we describe the rapid social evolution of player-developed folding algorithms that took place in the year following the introduction of these tools. Players developed over 5,400 different recipes, both by creating new algorithms and by modifying and recombining successful recipes developed by other players. The most successful recipes rapidly spread through the Foldit player population, and two of the recipes became particularly dominant. Examination of the algorithms encoded in these two recipes revealed a striking similarity to an unpublished algorithm developed by scientists over the same period. Benchmark calculations show that the new algorithm independently discovered by scientists and by Foldit players outperforms previously published methods. Thus, online scientific game frameworks have the potential not only to solve hard scientific problems, but also to discover and formalize effective new strategies and algorithms.

The shape of proteins is a really useful thing to know. If you are in drug research, it can help you find molecules that can manipulate a protein to kill a pathogen or repair a fault in a patient’s body. If you study evolution, it can help you find deep relationships among proteins that sequence similarities no longer preserve, and understand how their intricate workings evolved.

Traditionally, there have been two good ways of determining the structure of a protein. One is by purifying and crystallising it, and shooting X-rays at the crystals. Obviously, that only works with proteins that can be purified and crystallised, which is not all of them. The other is homology-based prediction – basically comparison with a related protein of known structure, which obviously requires a similar enough protein with a known structure.

Predicting the structure of a protein from its amino acid sequence is fiendishly difficult, but that’s what the folks behind Rosetta and Foldit are trying to do. Nowadays, isolating and sequencing the gene that codes for your protein of interest is relatively easy (sequencing the protein itself is tougher). If all you had to do to accurately know its structure was to plug the sequence into a program and wait a few minutes, that would make the life of many people much easier.

(I briefly played Foldit, but I admit I jut got lost and frustrated and gave up. However, I encourage everyone with an actual attention span to give it a go and see if it’s for you.)

We all know how great cephalopods are at camouflage. An octopus can meld seamlessly into just about any realistic environment. Deep-sea squid are known to change the colour of the light they emit to match the colour of their surroundings.

Now here are a couple of cephalopods that switch from transparent to coloured and back in the blink of an eye. According to Zylinski and Johnsen (2011), this allows them to sort of have the cake and eat it in the very special habitat they share: the “twilight zone” of the ocean.

Twilight zone creatures, you see, face a dilemma. This is the depth at which some light from above may penetrate depending on the circumstances, but many organisms make their own light to hunt and communicate. The best way to stay hidden from the (mainly blue) headlights of deep-sea predators is to be red or black – but being dark means that the faint light from above exposes your silhouette to predators below you.

And the best way not to have a silhouette – i.e. letting ambient light through you – makes you positively shine in a strong, directed beam of blue light. No transparent animal is completely transparent, and much of the light you shine on them bounces straight back at the source – which is likely to be out for a nice juicy meal of octopus.

This challenge is a piece of cake for masters of camouflage like cephalopods, apparently. When simply swimming around in ambient light, the octopus Japetella heathi and the squid Onychoteuthis banksii are mostly transparent. Shine blue light on them, though, and they are covered in reddish spots faster than you can say “red” (red light and a variety of other stimuli don’t cause such a response). Just to be sure, the researchers also measured the animals’ reflectance – and sure enough, the dark versions reflected much less blue light than the “transparent” ones. The trick seems to work.

Like all cephalopod camouflage tricks, this one looks damned impressive. I don’t know if the videos uploaded with the article can be accessed without subscription, but if they can, they are well worth a look!

Also, Japetella is absolutely adorable 😀

Reference and image source:

Zylinski S and Johnsen S (2011) Mesopelagic cephalopods switch between transparency and pigmentation to optimize camouflage in the deep. Current Biology, in press

This is a quickie to share something randomly fascinating, courtesy of Schnakenberg et al. (2011). Their study looked at the effect of killing a certain cell type in the sperm storage organs of female fruit flies. They mainly looked at the effect of this on things like, well, sperm storage, sperm behaviour, number of eggs the females laid.

Experimental flies weren’t as good at laying eggs as normal females, and the reason for this is the really interesting bit. The eggs were fully formed and by all accounts, normal – they just got stuck inside the mother. And kept developing, to the point where the researchers could coax nearly-hatched eggs with wriggling maggots inside from the females.

I can’t go all “ha! this is how live birth evolves!” at creationists, since none of these maggots were actually born without the experimenters messing with their mothers. Still, that’s the sort of surprise I would like to see when I do creepy things to innocent little animals!